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Wednesday, November 25, 2015

Vestigial genes

I'd like to make a few more observations regarding Dennis Venema's arguments for human evolution. I don't claim to be an expert, but since he's writing for laymen, I will give a layman's reaction. Let's begin with a general point:

1. Depending on what you read, it might seem like the creationist (i.e. young-earth creationist, old-earth creationist, and/or ID-theorist) has no positive evidence for his position. He's simply poking holes in evolutionary theory. His arguments are essentially reactionary. And he posits ad hoc explanations to reconcile his position with the evidence.

But to my knowledge, there is no direct evidence for the theory of evolution (i.e. macroevolution/universal common descent). An evolutionary biologist or paleontologist attempts to retroengineer the natural history of life on earth based on living organisms.

The ostensible evidence for evolution is based on fossils, comparative anatomy, and (more recently) comparative genetics.

i) Problem with fossil evidence is that:

a) The appeal is circular: it presumes these are in fact transitional forms.

b) The fossils are widely separated in time and/or space. Often millions of years apart (on conventional dating). So any lineage must be postulated.

c) Variations are consistent with creationism.

ii) I find the appeal to comparative anatomy fallacious. An obvious reason why two different species have similar organs or body parts is because they perform the same function. For instance, dogs and cheetahs have similar paws because both hunt by running, and not because cheetahs are more closely related to dogs than cats.

Likewise, bats and whales both use echolocation to navigate, not because they are related to each other, but because they operate in darkness.

iii) Consider this in reverse: why is the body plan of an anteater so different than most other animals? Not because it's more distantly related, but because it needs that body plan to capitalize on a particular food niche.

Both similarities and dissimilarities have the same underlying explanation. If we don't explain why an anteater is dissimilar based on more distant common ancestry, we shouldn't explain why apes and humans are more similar based on more recent common ancestry. In both cases, design is indexed to function: common design=common function. Monkeys and raccoons have the kinds of paws they do to climb, manipulate food, in that type of environment.

2. Regarding Venema's specific evidence:

i) From a creationist standpoint, a gene might become vestigial through disuse. That would be analogous to say, blind cave fish. And that's consistent with creationism.

However, you might have a dormant gene that isn't in use, but is available for future use, should the occasion arise.

However, my body is able to produce a temporary suntan. And that can come in handy. If I couldn't develop a suntan, my skin would burn, and becoming increasingly burned, the more time I spend in direct sunshine without covering (e.g. during the summer months).

Now, even if my N. European ancestors rarely had occasion to take advantage of that potential, it can be very useful to have. Suppose I move from Switzerland to the sunbelt, and spend lots of time out of doors. The ability to form a suntan protects my skin from chronic burning. (Sure, there's still the risk of skin cancer from prolonged exposure.) Albinos are at high risk of sunburn.

ii) Air-based olfaction would be useful for orcas. They prowl the coastline for places where penguins and seals congregate. Being able to sense their presence on land by scent would help to locate prey. Even if they don't presently have a sense of smell, it might be useful for them to have the wherewithal to produce it.

I believe there's a debate about whether whales have a sense of smell:

iii) I've read that Mojave rattlesnake venom is more hemotoxic or neurotoxic depending on the geography. That shows the value of having an undeveloped genetic potential. What may be useless at one time or place may become useful at another.

b. There are also questions about how the molecular/genetic and organ/structure levels relate to one another, influence one another, etc. This is stuff scientists, physicians, and others still have a long way to go on.

c. Focusing on the molecular/genetic level, we can look at our DNA. Our DNA is approximately 2% (give or take) genetic plus 98% (give or take) "junk DNA." (And the definition of "junk DNA" seems to have changed over time and in different contexts.)

d. Focusing on junk DNA, we're still learning a lot about what junk DNA is, what it does, etc.

e. Junk DNA is made up of a lot of different stuff. One of these things in junk DNA is the non-coding genes aka pseudogenes.

3. Focusing on pseudogenes, a standard neo-Darwinian argument is pseudogenes were genes which were once functional but are now non-functional. Genes which have lost their original function from an ancestral gene(s). Or, as Jerry Coyne calls pseudogenes - "dead genes."

4. However:

a. There's evidence many pseudogenes are functional. ID theorists and others have pointed this out time and time again.

b. A pseudogene may have lost its original function but "picked up" another function.

c. If a gene is non-functional, it may not necessarily be vestigial, for a non-functional gene may not necessarily have had a formerly functional ancestral gene. Rather, perhaps the non-functional gene has always been non-functional. Although I suppose the evolutionist could ask, why would God have made a gene which has always been non-functional? But does everything have to have a function? Perhaps it's aesthetic.

5. A better way to frame it than non-functional vs. functional - and in fact the way it's framed by the more sophisticated evolutionists like Ernsy Mayr, if I recall - is non-coding vs. coding genetic material. That is, pseudogenes could be non-coding but still functional in other ways.

6. All that said, the key point, which is Steve's main idea (or at least consistent with his main idea), is that it is possible for non-coding DNA to become coding.

7. Regarding skin color. The most important factor in determining skin color is melanin. Melanin is a pigment produced by cells called melanocytes. Melanocytes produce melanin, and melanin is stored in cellular structures called melanosomes.

What's interesting is the number of melanocytes is basically the same in all races.

However, whereas in light colored people (e.g. whites) melanosomes are mostly concentrated in the basal layer of the skin, in dark colored people (e.g. blacks) melanosomes are present throughout all the layers of the skin.

8. Another thing that comes to mind is something evolutionist James Shapiro argues. Shapiro argues the genome is (or at least is like) a read-write storage system. And that a cell can rewrite its genome.

People like Coyne think this is kooky or loopy, as if cells have a mind of their own. Although we don't have to go this far, I don't think.

I think we could take it in terms of systems biology. That is, we could assess a creature or animal in terms of systems engineering concepts and processes (e.g. design, architecture, information, data flow).

I think it's important to remember, if a concern arises about the "reactive" nature of one's response to the alleged arguments for common ancestry (e.g., between man and apes) is that the prima facie case for some version of creationism is quite strong, and the developed case (e.g., with further ID argument) overwhelmingly strong. On the prima facie case, I believe it was Richard Dawkins himself, the arch-evolutionist, who said outright that Darwinism explains how things can come into being that *look designed* though they are not! Although Paley is much ridiculed these days, he had a good point as far as making the prima facie case for creation in something like the camera eye. I would even argue that lever joints and the gross structure of all major organs (think of the ear or the heart) make such a prima facie case.

As for common ancestry, there is, again, a good prima facie case against it in the overwhelming and evident differences between ourselves and apes. This may seem chiefly a matter of mental capacities, but the physical structures (such as the brain) support these mental capacities and their out-working in the world.

Then there is the mountain of evidence for design produced at the deeper, microscopic level, from the DNA code, the organelles of the cell, the incredibly complex and perfect interaction of body chemistry in processes like reproduction and the blood-clotting cascade, and so on almost ad infinitum.

It is in *this* context that the lists of pseudogenes on which Venema depends must be placed. They come as claimed evidence for the development of radically different species by natural processes amidst an existing wealth of evidence that some incredibly powerful and intelligent being intervened to create the creatures and life forms on earth--not just here or there, not just to kick things off, but in biological system after biological system, structure after structure. (Human beings and fish have radically different blood clotting systems, for example.) That being the case, the burden of proof is pretty solidly on the advocate of common ancestry to explain why we should _not_ believe that humans, already known to be so different from apes, were specially created.

Venema's type of arguments are supposed to supply that answer, and it is _then_ that one responds to them. Hence, the argument against common ancestry was, in a sense, already in place, and the response to these types of claims from genetic similarity can appear reactive only if one is looking at an unnecessarily isolated slice of the overall dialectical situation.

As Rocking mentioned, though, it turns out that Venema's whole argument relies on pseudogenes, and the increasing failure of the junk DNA claim makes, IMO, all such arguments shaky. In short, it can no longer be regarded as ad hoc at all to guess that pseudogenes are doing something and need to be the way they are for their function. And if that is the case, then the entire argument that they must be the leftover record of accidents of mutation that happened in our distant, common ancestral past with bonobos or chimps falls flat.

Really good points about the context of the debate, burden of proof, why our arguments are "reactive" given all this, etc.

I entirely agree with what you've about the "mountain of [scientific] evidence" as well. We have an embarrassing amount of riches here.

As a side note, if we take a step or two back, I think there are some fundamental disagreements between scientists (in different camps) over definitions as well. For example, I alluded to his above in how best to frame the debate over pseudogenes (non-functional vs. non-coding). There are likewise some disagreements between scientists over how best to define "gene," how best to demarcate the boundaries of three main types of pseudogenes (duplicated, processed, unitary), etc. Much of the argument depends on where we draw the lines. Point being, we don't necessarily have to play by the neo-Darwinist's rules and terms and so forth.